Since his playing career ended, Jones has had a long career as a minor league manager in the Rangers organization. He was a member of the Rangers' big league coaching staff in 2000 and 2001 and returned to the majors in 2006 as the team's first base coach. After the 2006 season, Jones returned to the minors as skipper of the Oklahoma RedHawks. On August 13, 2011, he earned his 1,500th victory as a minor league manager when his Round Rock Express defeated the Sacramento RiverCats, 6-3, in a Pacific Coast League game. Every one of those victories had been earned while managing in the Rangers' system.